Using Random Forest classification

Endothelial cells

## Using CANARY as id variables

## Confusion Matrix and Statistics
## 
##           Reference
## Prediction    G    P
##          G  226  143
##          P  153 1031
##                                          
##                Accuracy : 0.8094         
##                  95% CI : (0.789, 0.8287)
##     No Information Rate : 0.756          
##     P-Value [Acc > NIR] : 2.813e-07      
##                                          
##                   Kappa : 0.4788         
##                                          
##  Mcnemar's Test P-Value : 0.6009         
##                                          
##             Sensitivity : 0.5963         
##             Specificity : 0.8782         
##          Pos Pred Value : 0.6125         
##          Neg Pred Value : 0.8708         
##               Precision : 0.6125         
##                  Recall : 0.5963         
##                      F1 : 0.6043         
##              Prevalence : 0.2440         
##          Detection Rate : 0.1455         
##    Detection Prevalence : 0.2376         
##       Balanced Accuracy : 0.7373         
##                                          
##        'Positive' Class : G              
## 

Fibroblasts and Mesenchymal cells

## Using CANARY as id variables

## Confusion Matrix and Statistics
## 
##           Reference
## Prediction    G    P
##          G  634  243
##          P  366 6787
##                                           
##                Accuracy : 0.9242          
##                  95% CI : (0.9182, 0.9299)
##     No Information Rate : 0.8755          
##     P-Value [Acc > NIR] : < 2.2e-16       
##                                           
##                   Kappa : 0.6328          
##                                           
##  Mcnemar's Test P-Value : 7.666e-07       
##                                           
##             Sensitivity : 0.63400         
##             Specificity : 0.96543         
##          Pos Pred Value : 0.72292         
##          Neg Pred Value : 0.94883         
##               Precision : 0.72292         
##                  Recall : 0.63400         
##                      F1 : 0.67555         
##              Prevalence : 0.12453         
##          Detection Rate : 0.07895         
##    Detection Prevalence : 0.10922         
##       Balanced Accuracy : 0.79972         
##                                           
##        'Positive' Class : G               
## 

T cells

## Using CANARY as id variables

## Confusion Matrix and Statistics
## 
##           Reference
## Prediction     G     P
##          G  1359  1324
##          P   797 15672
##                                           
##                Accuracy : 0.8893          
##                  95% CI : (0.8847, 0.8937)
##     No Information Rate : 0.8874          
##     P-Value [Acc > NIR] : 0.2155          
##                                           
##                   Kappa : 0.4992          
##                                           
##  Mcnemar's Test P-Value : <2e-16          
##                                           
##             Sensitivity : 0.63033         
##             Specificity : 0.92210         
##          Pos Pred Value : 0.50652         
##          Neg Pred Value : 0.95161         
##               Precision : 0.50652         
##                  Recall : 0.63033         
##                      F1 : 0.56169         
##              Prevalence : 0.11257         
##          Detection Rate : 0.07096         
##    Detection Prevalence : 0.14009         
##       Balanced Accuracy : 0.77622         
##                                           
##        'Positive' Class : G               
## 

CD8+ T cells

## Using CANARY as id variables

## Confusion Matrix and Statistics
## 
##           Reference
## Prediction    G    P
##          G  526  284
##          P  205 3841
##                                           
##                Accuracy : 0.8993          
##                  95% CI : (0.8905, 0.9076)
##     No Information Rate : 0.8495          
##     P-Value [Acc > NIR] : < 2.2e-16       
##                                           
##                   Kappa : 0.623           
##                                           
##  Mcnemar's Test P-Value : 0.0004198       
##                                           
##             Sensitivity : 0.7196          
##             Specificity : 0.9312          
##          Pos Pred Value : 0.6494          
##          Neg Pred Value : 0.9493          
##               Precision : 0.6494          
##                  Recall : 0.7196          
##                      F1 : 0.6827          
##              Prevalence : 0.1505          
##          Detection Rate : 0.1083          
##    Detection Prevalence : 0.1668          
##       Balanced Accuracy : 0.8254          
##                                           
##        'Positive' Class : G               
## 

CD4+ T cells

## Using CANARY as id variables

## Confusion Matrix and Statistics
## 
##           Reference
## Prediction    G    P
##          G  453  516
##          P  198 5943
##                                           
##                Accuracy : 0.8996          
##                  95% CI : (0.8924, 0.9065)
##     No Information Rate : 0.9084          
##     P-Value [Acc > NIR] : 0.9951          
##                                           
##                   Kappa : 0.505           
##                                           
##  Mcnemar's Test P-Value : <2e-16          
##                                           
##             Sensitivity : 0.69585         
##             Specificity : 0.92011         
##          Pos Pred Value : 0.46749         
##          Neg Pred Value : 0.96776         
##               Precision : 0.46749         
##                  Recall : 0.69585         
##                      F1 : 0.55926         
##              Prevalence : 0.09156         
##          Detection Rate : 0.06371         
##    Detection Prevalence : 0.13629         
##       Balanced Accuracy : 0.80798         
##                                           
##        'Positive' Class : G               
## 

Myeloid cells

## Using CANARY as id variables

## Confusion Matrix and Statistics
## 
##           Reference
## Prediction    G    P
##          G  783  301
##          P  214 5597
##                                           
##                Accuracy : 0.9253          
##                  95% CI : (0.9188, 0.9314)
##     No Information Rate : 0.8554          
##     P-Value [Acc > NIR] : < 2.2e-16       
##                                           
##                   Kappa : 0.7086          
##                                           
##  Mcnemar's Test P-Value : 0.0001509       
##                                           
##             Sensitivity : 0.7854          
##             Specificity : 0.9490          
##          Pos Pred Value : 0.7223          
##          Neg Pred Value : 0.9632          
##               Precision : 0.7223          
##                  Recall : 0.7854          
##                      F1 : 0.7525          
##              Prevalence : 0.1446          
##          Detection Rate : 0.1136          
##    Detection Prevalence : 0.1572          
##       Balanced Accuracy : 0.8672          
##                                           
##        'Positive' Class : G               
## 

NK cells

## Using CANARY as id variables

## Confusion Matrix and Statistics
## 
##           Reference
## Prediction   G   P
##          G 344  52
##          P  65 814
##                                          
##                Accuracy : 0.9082         
##                  95% CI : (0.891, 0.9235)
##     No Information Rate : 0.6792         
##     P-Value [Acc > NIR] : <2e-16         
##                                          
##                   Kappa : 0.7876         
##                                          
##  Mcnemar's Test P-Value : 0.2673         
##                                          
##             Sensitivity : 0.8411         
##             Specificity : 0.9400         
##          Pos Pred Value : 0.8687         
##          Neg Pred Value : 0.9261         
##               Precision : 0.8687         
##                  Recall : 0.8411         
##                      F1 : 0.8547         
##              Prevalence : 0.3208         
##          Detection Rate : 0.2698         
##    Detection Prevalence : 0.3106         
##       Balanced Accuracy : 0.8905         
##                                          
##        'Positive' Class : G              
## 

Epithelial cells

## Using CANARY as id variables

## Confusion Matrix and Statistics
## 
##           Reference
## Prediction     G     P
##          G  1766   687
##          P   710 15185
##                                           
##                Accuracy : 0.9239          
##                  95% CI : (0.9199, 0.9277)
##     No Information Rate : 0.8651          
##     P-Value [Acc > NIR] : <2e-16          
##                                           
##                   Kappa : 0.6726          
##                                           
##  Mcnemar's Test P-Value : 0.5561          
##                                           
##             Sensitivity : 0.71325         
##             Specificity : 0.95672         
##          Pos Pred Value : 0.71993         
##          Neg Pred Value : 0.95533         
##               Precision : 0.71993         
##                  Recall : 0.71325         
##                      F1 : 0.71658         
##              Prevalence : 0.13495         
##          Detection Rate : 0.09625         
##    Detection Prevalence : 0.13369         
##       Balanced Accuracy : 0.83498         
##                                           
##        'Positive' Class : G               
## 

Comparing Median expression of each marker per cell type

Endothelial cells

## Using CANARY, pt_ID as id variables

##              Protein    p.value FDR_corrected
## 1        141Pr_EpCAM 0.47070551     0.5824502
## 2       142Nd_ccasp3 0.95892310     0.9589231
## 3      144Nd_HLA-ABC 0.17614084     0.5724070
## 4         145Nd_CD31 0.32258717     0.5824502
## 5  146Nd_Thioredoxin 0.23168319     0.5724070
## 6        147Sm_b-CAT 0.74318872     0.7823039
## 7         151Eu_TTF1 0.35278528     0.5824502
## 8         153Eu_Ki67 0.25608663     0.5724070
## 9         154Sm_CD45 0.22168819     0.5724070
## 10    156Gd_Vimentin 0.27468896     0.5724070
## 11     158Gd_p-STAT3 0.47913331     0.5824502
## 12         159Tb_CD4 0.18101154     0.5724070
## 13        160Gd_MDM2 0.49508264     0.5824502
## 14 161Dy_Cytokeratin 0.28620351     0.5724070
## 15         162Dy_MET 0.44735653     0.5824502
## 16        163Dy_TP63 0.02102468     0.4204935
## 17         164Dy_CK7 0.09186981     0.5724070
## 18        165Ho_EGFR 0.37935787     0.5824502
## 19      174Yb_HLA-DR 0.11165386     0.5724070
## 20       175Lu_PD-L1 0.67040646     0.7448961

Fibroblasts/Mesenchymal cells

## Using CANARY, pt_ID as id variables

##              Protein     p.value FDR_corrected
## 1        141Pr_EpCAM 0.251800611     0.4333774
## 2       142Nd_ccasp3 0.606497326     0.7412745
## 3      144Nd_HLA-ABC 0.917901965     0.9197583
## 4         145Nd_CD31 0.718163959     0.7899804
## 5        147Sm_b-CAT 0.216247330     0.4333774
## 6         151Eu_TTF1 0.359097978     0.5266770
## 7         153Eu_Ki67 0.256086630     0.4333774
## 8         154Sm_CD45 0.511298970     0.6616810
## 9         155Gd_CD56 0.919758300     0.9197583
## 10    156Gd_Vimentin 0.052045561     0.3278738
## 11     158Gd_p-STAT3 0.511298970     0.6616810
## 12         159Tb_CD4 0.100989632     0.3278738
## 13        160Gd_MDM2 0.119226847     0.3278738
## 14 161Dy_Cytokeratin 0.286203511     0.4497484
## 15         162Dy_MET 0.230376074     0.4333774
## 16        163Dy_TP63 0.094703337     0.3278738
## 17         164Dy_CK7 0.038040141     0.3278738
## 18        165Ho_EGFR 0.114680175     0.3278738
## 19        166Er_CD44 0.101930635     0.3278738
## 20         170Yb_CD3 0.699267261     0.7899804
## 21        172Yb_p-S6 0.135245907     0.3306011
## 22      174Yb_HLA-DR 0.007813437     0.1718956

Immune cells

## Using CANARY, pt_ID as id variables

##           Protein    p.value FDR_corrected
## 1     141Pr_EpCAM 0.30270519     0.5900982
## 2   144Nd_HLA-ABC 0.17815278     0.5302752
## 3      145Nd_CD31 0.12074819     0.4469706
## 4      151Eu_TTF1 0.73699603     0.8206337
## 5      153Eu_Ki67 0.42322718     0.5900982
## 6      154Sm_CD45 0.12415850     0.4469706
## 7  156Gd_Vimentin 0.01538856     0.2769940
## 8   158Gd_p-STAT3 0.20691654     0.5302752
## 9       159Tb_CD4 0.23567786     0.5302752
## 10     160Gd_MDM2 0.47084087     0.6053668
## 11      162Dy_MET 0.42273745     0.5900982
## 12     163Dy_TP63 0.82063372     0.8206337
## 13      164Dy_CK7 0.51005544     0.6120665
## 14     165Ho_EGFR 0.42618206     0.5900982
## 15     166Er_CD44 0.41810901     0.5900982
## 16      170Yb_CD3 0.82063372     0.8206337
## 17    171Yb_CD11b 0.04341486     0.3907337
## 18   174Yb_HLA-DR 0.08454391     0.4469706

T cells

## Using CANARY, pt_ID as id variables

##           Protein    p.value FDR_corrected
## 1     141Pr_EpCAM 0.69584622     0.6958462
## 2   144Nd_HLA-ABC 0.05834773     0.3306371
## 3      145Nd_CD31 0.21259674     0.6004439
## 4      151Eu_TTF1 0.60262668     0.6402908
## 5      153Eu_Ki67 0.28256182     0.6004439
## 6      154Sm_CD45 0.04003110     0.3306371
## 7  156Gd_Vimentin 0.03035444     0.3306371
## 8       159Tb_CD4 0.42451245     0.6013926
## 9      160Gd_MDM2 0.58862222     0.6402908
## 10      162Dy_MET 0.40662831     0.6013926
## 11     163Dy_TP63 0.51129897     0.6402908
## 12      164Dy_CK7 0.08097799     0.3404075
## 13     165Ho_EGFR 0.58304927     0.6402908
## 14     166Er_CD44 0.10011984     0.3404075
## 15      168Er_CD8 0.38117376     0.6013926
## 16      170Yb_CD3 0.34837291     0.6013926
## 17   174Yb_HLA-DR 0.26763702     0.6004439

CD8 T cells

## Using CANARY, pt_ID as id variables

##              Protein     p.value FDR_corrected
## 1        141Pr_EpCAM 0.779100821     0.9364463
## 2      144Nd_HLA-ABC 0.004201291     0.1092336
## 3         145Nd_CD31 0.864411934     0.9364463
## 4         148Nd_HER2 0.064621030     0.3561469
## 5      150Nd_p-STAT5 0.937076506     0.9685137
## 6         151Eu_TTF1 0.798329996     0.9364463
## 7         153Eu_Ki67 0.348881570     0.8246292
## 8         154Sm_CD45 0.055597903     0.3561469
## 9         155Gd_CD56 0.085240901     0.3561469
## 10    156Gd_Vimentin 0.095885706     0.3561469
## 11         159Tb_CD4 0.394032207     0.8537364
## 12        160Gd_MDM2 0.847177570     0.9364463
## 13 161Dy_Cytokeratin 0.968513746     0.9685137
## 14         162Dy_MET 0.443515326     0.8870307
## 15        163Dy_TP63 0.198039328     0.5731536
## 16         164Dy_CK7 0.081171972     0.3561469
## 17        165Ho_EGFR 0.691734433     0.9364463
## 18        166Er_CD44 0.217233300     0.5731536
## 19       167Er_p-ERK 0.782667731     0.9364463
## 20         168Er_CD8 0.597706027     0.9364463
## 21        169Tm_CD24 0.076069146     0.3561469
## 22         170Yb_CD3 0.478294283     0.8882608
## 23       171Yb_CD11b 0.683747538     0.9364463
## 24        172Yb_p-S6 0.664654705     0.9364463
## 25      174Yb_HLA-DR 0.536993609     0.9307889
## 26       175Lu_PD-L1 0.220443712     0.5731536

CD4 T cells

## Using CANARY, pt_ID as id variables

##              Protein     p.value FDR_corrected
## 1        141Pr_EpCAM 0.875266433     0.9336175
## 2      144Nd_HLA-ABC 0.088468197     0.2830982
## 3         151Eu_TTF1 0.533691210     0.7115883
## 4         153Eu_Ki67 0.307529890     0.4920478
## 5         154Sm_CD45 0.084543911     0.2830982
## 6     156Gd_Vimentin 0.007139752     0.1142360
## 7          159Tb_CD4 0.361721725     0.5261407
## 8         160Gd_MDM2 0.801083915     0.9155245
## 9  161Dy_Cytokeratin 0.979433173     0.9794332
## 10         162Dy_MET 0.229653274     0.4490272
## 11        163Dy_TP63 0.231683186     0.4490272
## 12         164Dy_CK7 0.126909027     0.3384241
## 13        165Ho_EGFR 0.656256661     0.8077005
## 14        166Er_CD44 0.042801717     0.2830982
## 15         170Yb_CD3 0.252577790     0.4490272
## 16      174Yb_HLA-DR 0.084434343     0.2830982

Myeloid cells

## Using CANARY, pt_ID as id variables

##              Protein     p.value FDR_corrected
## 1        141Pr_EpCAM 0.519696825    0.73368963
## 2      144Nd_HLA-ABC 0.327013456    0.62751609
## 3         145Nd_CD31 0.877203626    0.93891013
## 4  146Nd_Thioredoxin 0.958908228    0.95890823
## 5        147Sm_b-CAT 0.302196788    0.62751609
## 6         151Eu_TTF1 0.502686766    0.73368963
## 7         153Eu_Ki67 0.339904550    0.62751609
## 8         154Sm_CD45 0.084543911    0.35594601
## 9         155Gd_CD56 0.335327658    0.62751609
## 10    156Gd_Vimentin 0.084543911    0.35594601
## 11     158Gd_p-STAT3 0.801083915    0.93891013
## 12         159Tb_CD4 0.003921026    0.09376124
## 13        160Gd_MDM2 0.152242116    0.45672635
## 14 161Dy_Cytokeratin 0.241979190    0.62751609
## 15         162Dy_MET 0.088986503    0.35594601
## 16        163Dy_TP63 0.463456332    0.73368963
## 17         164Dy_CK7 0.125389877    0.42990815
## 18        165Ho_EGFR 0.072586747    0.35594601
## 19        166Er_CD44 0.899788877    0.93891013
## 20         170Yb_CD3 0.596163603    0.77538141
## 21       171Yb_CD11b 0.403568549    0.69183180
## 22        172Yb_p-S6 0.613843615    0.77538141
## 23      174Yb_HLA-DR 0.007813437    0.09376124
## 24       175Lu_PD-L1 0.840290669    0.93891013

NK cells

## Using CANARY, pt_ID as id variables

##              Protein     p.value FDR_corrected
## 1        141Pr_EpCAM 0.743188717     0.8617875
## 2       142Nd_ccasp3 0.762350452     0.8617875
## 3      144Nd_HLA-ABC 0.062807797     0.3266005
## 4         145Nd_CD31 0.448056957     0.8448014
## 5  146Nd_Thioredoxin 0.246484993     0.8448014
## 6        147Sm_b-CAT 0.416946389     0.8448014
## 7         148Nd_HER2 0.011611172     0.1509452
## 8      150Nd_p-STAT5 0.649847205     0.8448014
## 9         151Eu_TTF1 0.535889780     0.8448014
## 10       152Sm_p-AKT 0.527776242     0.8448014
## 11        153Eu_Ki67 0.360292858     0.8448014
## 12        154Sm_CD45 0.089513314     0.3878910
## 13        155Gd_CD56 1.000000000     1.0000000
## 14    156Gd_Vimentin 0.021024677     0.1822139
## 15     158Gd_p-STAT3 0.495082636     0.8448014
## 16         159Tb_CD4 1.000000000     1.0000000
## 17        160Gd_MDM2 0.631740961     0.8448014
## 18 161Dy_Cytokeratin 0.879879917     0.9532032
## 19         162Dy_MET 0.486698306     0.8448014
## 20        163Dy_TP63 0.561488287     0.8448014
## 21         164Dy_CK7 0.757285150     0.8617875
## 22        165Ho_EGFR 0.350524782     0.8448014
## 23        166Er_CD44 0.613843615     0.8448014
## 24        172Yb_p-S6 0.028599489     0.1858967
## 25      174Yb_HLA-DR 0.004459218     0.1159397
## 26       175Lu_PD-L1 0.439747569     0.8448014

Epithelial cells

## Using CANARY, pt_ID as id variables

##              Protein    p.value FDR_corrected
## 1        141Pr_EpCAM 0.25716783     0.5071181
## 2       142Nd_ccasp3 0.21199182     0.5071181
## 3      144Nd_HLA-ABC 0.30144693     0.5167662
## 4         145Nd_CD31 0.21449027     0.5071181
## 5  146Nd_Thioredoxin 0.91795032     0.9197583
## 6        147Sm_b-CAT 0.14213323     0.5071181
## 7         148Nd_HER2 0.03492253     0.2793803
## 8      150Nd_p-STAT5 0.52777624     0.7037017
## 9         151Eu_TTF1 0.68025814     0.8163098
## 10        153Eu_Ki67 0.12805732     0.5071181
## 11        154Sm_CD45 0.17614084     0.5071181
## 12        155Gd_CD56 0.02343785     0.2793803
## 13    156Gd_Vimentin 0.38932196     0.6229151
## 14     158Gd_p-STAT3 0.80108392     0.8739097
## 15         159Tb_CD4 0.23533821     0.5071181
## 16        160Gd_MDM2 0.25257779     0.5071181
## 17 161Dy_Cytokeratin 0.02267177     0.2793803
## 18         162Dy_MET 0.41810901     0.6271635
## 19        163Dy_TP63 0.78165245     0.8739097
## 20         164Dy_CK7 0.27468896     0.5071181
## 21        165Ho_EGFR 0.62440628     0.7887237
## 22         170Yb_CD3 0.91975830     0.9197583
## 23      174Yb_HLA-DR 0.10471596     0.5071181
## 24       175Lu_PD-L1 0.50268677     0.7037017